GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08235 in Herbaspirillum seropedicae SmR1

Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate HSERO_RS05960 HSERO_RS05960 ABC transporter permease

Query= reanno::azobra:AZOBR_RS08235
         (301 letters)



>FitnessBrowser__HerbieS:HSERO_RS05960
          Length = 309

 Score =  258 bits (658), Expect = 2e-73
 Identities = 133/307 (43%), Positives = 207/307 (67%), Gaps = 18/307 (5%)

Query: 1   MEYFLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVAL-----ITFL 55
           M+ F+QQ+INGL LG++Y LIA+GYTMVYG++ +INFAHG+I M+GA V L     +  +
Sbjct: 1   MDIFIQQIINGLVLGSMYALIALGYTMVYGVLNLINFAHGDILMVGAMVGLSLLKVVQQV 60

Query: 56  AIGSLGITWVPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQ 115
           A G  GI    + L++ +V ++    V    +ERIAYRPLR++PRLAPLI+AIG+SI LQ
Sbjct: 61  APGLPGI----VQLVIAIVGAIPVCIVVSLLIERIAYRPLRNAPRLAPLITAIGVSILLQ 116

Query: 116 NYVQILQGARSKPLQPILPGNLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGR 175
               ++ G    P   ++P +   + GA+ +S  ++  + + +  M G   ++ +T +GR
Sbjct: 117 TLAMMIWGRSPLPFPQVMPSDPVHIAGAL-ISPTQIMLLALAVLAMVGLVLIVEKTKMGR 175

Query: 176 AQRACEQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKA 235
           A RA  ++ ++AGL+GV+ ++VI +TF +GA LAA+AG+M    Y    F +GF+ G+KA
Sbjct: 176 AMRATAENPRIAGLMGVDANKVIVVTFAIGAGLAAIAGVMWAANYSTAQFAMGFVPGLKA 235

Query: 236 FTAAVLGGIGSLPGAMLGGVVIGLIEAFWSGY--------MGSEWKDVATFTILVLVLIF 287
           F+AAVLGGIG++ GAMLGG+++GLIE+  +GY        +GS ++D+  F +L++VL  
Sbjct: 236 FSAAVLGGIGNIYGAMLGGILLGLIESLGAGYIGDLTGNFLGSNYQDIFAFIVLIIVLTL 295

Query: 288 RPTGLLG 294
           RP+G++G
Sbjct: 296 RPSGIMG 302


Lambda     K      H
   0.329    0.144    0.425 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 396
Number of extensions: 17
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 301
Length of database: 309
Length adjustment: 27
Effective length of query: 274
Effective length of database: 282
Effective search space:    77268
Effective search space used:    77268
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory